So I have the pleasure to travel to MAN and LON in the near future. Unfortunately (only because it is a 4-hour detour), based on flight availability, I'm flying IAD-MAN via MUC. I've never made a connection on the Europe side, only on the US side. So I'm very confused right now, and the Munich Airport website is an exercise in futility.

This is what I know. We will arrive in MUC on a flight from the US (outside the EU). Therefore, our bags will not have the pretty green strips on the bag tags. I expect those will transfer automatically and we will clear customs in the UK.

Now, our flight from MUC-MAN is intra-EU but not intra-Schengen. So we will go through passport control upon arrival in MAN. Will we also have to go through passport control in MUC? In other words, I assume that our flight from the US will arrive in some sort of international sterile area. Will the flight to MAN leave from that same sterile area? Or, because it is an intra-EU flight, will it depart from some other part of Terminal 2 that will require us to clear some sort of controls into Germany first?

Flights in Germany are separated Schengen/non-Schengen, so whether it's inside the EU or not does not matter. What matters in Schengen. So no, you will not have to clear passport control, and your bags will go directly to MAN, without the green stripes.